Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate 8501897 DvMF_2612 pyruvate carboxyltransferase (RefSeq)
Query= curated2:A3CUF2 (503 letters) >FitnessBrowser__Miya:8501897 Length = 455 Score = 193 bits (491), Expect = 9e-54 Identities = 140/378 (37%), Positives = 192/378 (50%), Gaps = 29/378 (7%) Query: 13 DTTLRDGEQTPGVSLTPAGKLEIATHLADVGVHVIEAGSAAAS-VGERESIRAIADAGLA 71 DTTLR+GEQ+ G L+ A + + LA VGV E G A + + ++ A GLA Sbjct: 4 DTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWAGREDLTDMLALSARVAPGLA 63 Query: 72 AECCTYVRALPGDIDLAADAGADSVHLVVPVSDLHIAKKLRKTREQVSEMAWSAVEYAKE 131 A + R PGD+ A GA V + VPVSD H+A++L R + ++ + + A+ Sbjct: 64 A--AAWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAEARM 121 Query: 132 RGLV-VELSGEDASRADQDFLAEVFREGVERGADRLCFCDTVGLLTPERAAAII------ 184 G+ V + EDASRAD+ F+ V GA R+ DTVGL TP A ++ Sbjct: 122 LGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRALRAE 181 Query: 185 ----------PPLLFAPLSIHCHDDLGFGLATTVAALRAGATCAHVTVNGLGERAGNTSL 234 P + H H+D G A + AL GA CA V+V GLGERAG L Sbjct: 182 LEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGVARL 241 Query: 235 EELVMALEVLYGVDTGIATEELYPLST---HVARLTGVPLATNKPIVGEMAFTHESGIHA 291 EEL AL V G A EL PL VA+ + + + P+ G F ESG+HA Sbjct: 242 EELAAALVV-----RGRARFELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHA 296 Query: 292 HGVMRDASTYEPLQPERVGRRRRIVLGKHSGSAAVEAALHDMGYAPSAAQLKEIVDRIKR 351 HGV RD S +EP PE VG RR+ +G+ SG AAV AAL ++ P +L IV+ ++ Sbjct: 297 HGVRRDPSLFEPFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRD 356 Query: 352 LGDAGMR-ITDADIMAIA 368 L R +T A++ +A Sbjct: 357 LSATLRRPLTPAELAEVA 374 Lambda K H 0.318 0.134 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 579 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 503 Length of database: 455 Length adjustment: 34 Effective length of query: 469 Effective length of database: 421 Effective search space: 197449 Effective search space used: 197449 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory